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Genome-wide development of lncRNA-derived-SSR markers for Dongxiang wild rice (Oryza rufipogon Griff.)

Published online by Cambridge University Press:  10 January 2022

Wanling Yang ,
Yuanwei Fan ,
Yong Chen ,
Gumu Ding ,
Hu Liu ,
Jiankun Xie  and
Fantao Zhang Open the ORCID record for Fantao Zhang [Opens in a new window]
Wanling Yang
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Yuanwei Fan
Affiliation:
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
Yong Chen
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Gumu Ding
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Hu Liu
Affiliation:
Huaian Zhuxiang Ecological Agriculture CO. LTD, Huaian 223299, Jiangsu Province, China
Jiankun Xie*
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
Fantao Zhang*
Affiliation:
Jiangxi Provincial Key Lab of Protection and Utilization of Subtropical Plant Resources, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
*
Author for correspondence: Fantao Zhang, E-mail: zhang84004@163.com; Jiankun Xie, E-mail: xiejiankun11@163.com
Author for correspondence: Fantao Zhang, E-mail: zhang84004@163.com; Jiankun Xie, E-mail: xiejiankun11@163.com
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Abstract

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is the northernmost distributed wild rice found in the world. Similar to other populations of O. rufipogon, DXWR contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in plant breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In our previous study, we obtained 1655 lncRNA transcripts from DXWR using strand-specific RNA sequencing. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice accessions. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research.

Keywords

Crop wild relativegenetic markergermplasm resourcelong non-coding RNAsimple repeat sequence
Type
Short Communication
Information
Plant Genetic Resources , Volume 19 , Issue 6 , December 2021 , pp. 549 - 552
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of NIAB

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Footnotes

*

These authors contributed equally to this work

†

Present address: Department of Biology and Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, MO 63130, USA

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